Which scenario will lead to the destruction of the Human Race, Man’s Inhumanity to Man, or the savage aberrations that now run wild in the 41st Century? Once again that question drives the plot for season two of the FOX series “Wayward Pines,” as the residents fight amongst each other, and the creatures humans evolved into due to toxic pollution. The secrecy that engulfed the town in the first season’s mostly gone, but the divisiveness remains, as the young, volatile and unstable zealot Jason Higgins, attempts to keep the citizens in line.

The action begins shortly after the final scene of the season premier, as we watch a van containing Dr. Theo Yedlin and two rebels get sent through the gate that protects the town. Yedlin, Ben Burke and Xander, split up and try to escape the Abbies, however Xander’s almost immediately pounced on. The Abbies keep rushing the electric fence, which at first seems like madness, but they’ve got a plan in mind.

As the creatures fall to their deaths, they form a mountain of corpses high enough for some of the Abbies to make it over the fence. Higgins orders troops to the fence and insists that he and his significant other Kerry travel out there to assess the situation. What he doesn’t count on is Kerry getting mauled by an Abbie that jumped the fence, meaning Jason had to save Yedlin, the only doctor in the town to keep Kerry alive.

Yedlin’s brought to the hospital and Higgins orders him to perform surgery on Kerry, but Theo says not so fast. Jason needs him so Theo says he’s not doing anything until his wife’s brought to the hospital and he gets an explanation of what’s going on. Rebecca’s brought to the facility but Yedlin demands to know where they’re at. Rebecca shakes her head at Higgins, but the leader tells her husband the truth, however Theo doesn’t believe him. Rebecca convinces her husband to perform the surgery and he saves Campbell.

After completing the operation, Theo and Rebecca head to a home with their name on the mailbox. Theo finds out that his wife was revived three years before. Yedlin finally starts to accept his reality, there’s a knock at the front door and it’s of their neighbor’s Nancy, with her son who’s feeling sick and heard Yedlin’s a doctor. Thus starts Theo’s career as head of medicine at Wayward Pines Hospital.

We meet a new character, a man who appears to be in his mid-forties named CJ Mitchum. He’s described as a protégé of Pilcher’s and apparently he’s in charge of the military. Higgins wants to meet with him to discuss harvesting the crops outside the fence. The soil within the town’s not suitable to grow vegetables, so they had to plant their crops outside the fence, making the harvest a life-threatening exercise. It’s decided that the soldiers will attempt to protect the harvesters with flame-throwers, hoping the weapons will fend off the Abbies. The plan works, after incinerating a few of the creatures the rest of the Abbies retreat and they’re able to harvest their crops.

Ben Burke grabs one of the harvesters and begs the guy to hide him in a truck as he’s a member of the First Generation of Wayward Pines. The guy throws Burke off him and scrambles into a truck. Ben runs after the vehicles but the gate slams shut just before he gets to it.

Yedlin arrives for his first full day at the hospital and gets greeted by the hospital’s receptionist, Arlene who used to be the receptionist for the Sheriff. Theo recognizes her from when he saw her receiving electro-shock treatments when he operated on Kate Hewson. Arlene calls them her little tune-up to balance her out and says she’s now right as rain. The medical students then arrive so Theo can lead them on rounds.

Over at Wayward Pines Academy, Megan Fisher displays an Abbie’s cadaver eliciting gasps from the students. She smiles and tells them they’re perfectly safe as the creature’s dead. She then excitedly tells the students the cadavers and the three Abbies they hold captive will be the key to finding their weaknesses. She asks the students if they’ve got any questions and one of the boys asks if the Abbie in front of them scaled the fence by climbing on the pile of other creatures? He then asks if it can happen again and Megan says no because they defeated the beasts.

Yedlin and Higgins get into a spitting match as Jason tries to order Theo around and the doctor stands up to him. Theo says Higgins may not think Yedlin can do his job, but they both realize Jason can’t save a patient. Higgins starts to rant to Kerry, but Campbell tells her boyfriend that they need Yedlin and if not for him she’d be dead. Jason starts to cry and says she’s right.

Theresa Burke finds out that Higgins sent Ben outside the fence and begs some members of the First Generation to go out there and look for her son. She says that its their first rule that no member of the First Generation can harm another. Mario finally tells her they have their orders and tells two of the soldiers to take her home.

Ben makes one final plea for his life as he talks to the security cameras outside the fence. He says as a member of the First Generation, he’s supposed to be protected. He then says if his mother can hear him, he realizes she thought he went too far but he just wanted to do the right thing. He then says to Higgins hopefully some good will come of Ben’s death as the residents may realize what kind of a leader Jason is. Higgins tells the operator to kill the feed.

The next morning Burke’s standing in a cornfield when he hears rustling. He optimistically calls out for Mario and then Xander. However he soon sees a band of Abbies heading towards him. His final words are sorry dad and then the pack jump him.

The final scene has Kerry walk in on Jason watching the security monitors and she asks what he’s looking at and he responds nothing. Then he beckons Campbell to take a look and all the Abbies appear to have vanished.